RegulonDB RegulonDB 10.6.3: Gene Form
   

cspD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

macB clpS cspD macA MqsA CRP CRP PhoP MqsA ppGpp terminator TSS_1039 TSS_1039 TSS_1038 TSS_1038 clpAp3 clpAp3 clpAp2 clpAp2 TSS_1037 TSS_1037 clpAp1 clpAp1 TSS_1036 TSS_1036 TSS_1035 (cluster) TSS_1035 (cluster) TSS_1034 (cluster) TSS_1034 (cluster) TSS_1033 (cluster) TSS_1033 (cluster) clpSp7 clpSp7 TSS_1032 TSS_1032 TSS_1031 (cluster) TSS_1031 (cluster) TSS_1030 TSS_1030 clpSp clpSp clpSp6 clpSp6 cspDp cspDp TSS_1029 TSS_1029 TSS_1028 (cluster) TSS_1028 (cluster) TSS_1027 TSS_1027 TSS_1026 TSS_1026

Gene      
Name: cspD    Texpresso search in the literature
Synonym(s): ECK0871, EG11111, b0880, cspH, ybjA
Genome position(nucleotides): 922366 <-- 922590 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.44
External database links:  
ASAP:
ABE-0002991
CGSC:
31688
ECHOBASE:
EB1102
ECOCYC:
EG11111
ECOLIHUB:
cspD
OU-MICROARRAY:
b0880
REGULONDB:
b0880
STRING:
511145.b0880
M3D: cspD
COLOMBOS: cspD
PortEco: b0880


Product      
Name: DNA replication inhibitor
Synonym(s): CspD, CspH, YbjA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 7.969
Isoelectric point: 6.224
Motif(s):
 
Type Positions Sequence
3 -> 65 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV
19 -> 19 C
4 -> 64 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVI

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
  3 - regulation --> 3.1 - type of regulation --> 3.1.1 - DNA structure level
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0090729 - toxin activity
GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003697 - single-stranded DNA binding
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0042803 - protein homodimerization activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0042594 - response to starvation
GO:0008156 - negative regulation of DNA replication
GO:0009405 - pathogenesis
Note(s): Note(s): ...[more].
Reference(s): [1] Xia B., et al., 2001
External database links:  
DIP:
DIP-47833N
ECOCYC:
EG11111-MONOMER
ECOLIWIKI:
b0880
INTERPRO:
IPR012340
INTERPRO:
IPR019844
INTERPRO:
IPR012751
INTERPRO:
IPR012156
INTERPRO:
IPR011129
INTERPRO:
IPR002059
MINT:
MINT-1219798
MODBASE:
P0A968
PFAM:
PF00313
PRIDE:
P0A968
PRINTS:
PR00050
PRODB:
PRO_000022341
PROSITE:
PS51857
PROSITE:
PS00352
PROTEINMODELPORTAL:
P0A968
REFSEQ:
NP_415401
SMART:
SM00357
SMR:
P0A968
SWISSMODEL:
P0A968
UNIPROT:
P0A968


Operon      
Name: cspD         
Operon arrangement:
Transcription unit        Promoter
cspD


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, H-NS
Repressed by: MqsA


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1026 921483 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1027 921911 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1028 (cluster) 922360 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1029 922660 forward nd [RS-EPT-CBR] [2]
  promoter clpSp6 922750 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_1030 922827 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1031 (cluster) 922831 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1032 922847 forward nd [RS-EPT-CBR] [2]
  promoter clpSp7 922912 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_1033 (cluster) 923059 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1034 (cluster) 923062 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1035 (cluster) 923067 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1036 923070 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1037 923091 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1038 923211 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1039 923214 forward nd [RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Xia B., Ke H., Inouye M., 2001, Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli., Mol Microbiol 40(1):179-88

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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